rs10104038

Positions:

• chr8-42673886-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0537 in 152,196 control chromosomes in the GnomAD database, including 275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.054 (275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8153 AN: 152076 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0531

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0537 AC: 8170 AN: 152196 Hom.: 275 Cov.: 32 AF XY: 0.0541 AC XY: 4022 AN XY: 74412

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0386

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0469 Hom.: 21

Bravo AF: 0.0533

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10104038; hg19: chr8-42529029;